Abstract 3106: Identifying drivers in the converging syntenic aneuploidies of spontaneous canine and pediatric high-grade glioma using imaging-based an arrayed CRISPR-Cas9 phenotypic screen
Authors: Samirkumar B. Amin, Amit Gujar, Eunhee Yi, Wonyeong Kang, Megan Costa, Greg Sjogren, Paul Gabriel, Leigh Maher, Peter Dickinson, Rebecca Packer, Elise Courtois, Paul Robson, Charles Lee, Roel Verhaak
Journal: Cancer Research (2022)

Abstract Gliomas occur in companion dogs at rates comparable to humans, with short-snouted breeds such as boxers being more susceptible than others. The natural progression of cancer in the immuno-competent host allows companion dogs diagnosed with sporadic glioma as an optimal model for preclinical testing of therapeutic approaches with human relevance, including immunotherapies. We have recently performed comprehensive genomic and epigenetic characterization of glioma in dogs to their human counterparts and found strong convergent evolution - shared somatic mutations and aneuploidies - among syntenic regions, including those of known pediatric glioma drivers, e.g., PDGFRA, MYC, PIK3CA. Here, using arrayed CRISPR-Cas9 imaging based phenotypic screen, we will probe potential oncogenic drivers and tumor suppressor genes within syntenic aneuploidies and thus outline functional versus non-functional heterogeneity of cancer aneuploidy. Specifically, we are conducting arrayed knockout screen (one gene per well) of 400+ genes within syntenic aneuploidies across primary cultured cells of canine glioma (n=2) and pediatric high-grade glioma cell lines (n=2). We will first capture images by high-speed confocal imaging system at three time points post-transduction of single guide RNAs (2 per gene) targeting each of 400+ genes in their separate wells. Then, using high-throughput image analysis and semi-supervised machine learning methods, we will measure well-based phenotypic features (viability, growth, and morphology) from these images. Genes will be ranked per cross-validated predicted probability in yielding either proliferating or slow-growing cell type based on learned phenotypic features using image data of knockout cells from and across wells. The top ranked genes will then be linked to oncogenes and tumor suppressors based on pathway and ontology analysis as well as further functional in vitro and in vivo (PDX) validation. We expect to find convergence of the most impactful molecular abnormalities (based on their knockout phenotypes) on candidate signaling pathways for the development of new drugs and repurposing of existing drugs for children and dogs with high-grade glioma. Citation Format: Samirkumar B. Amin, Amit Gujar, Eunhee Yi, Wonyeong Kang, Megan Costa, Greg Sjogren, Paul Gabriel, Leigh Maher, Peter Dickinson, Rebecca Packer, Elise Courtois, Paul Robson, Charles Lee, Roel Verhaak. Identifying drivers in the converging syntenic aneuploidies of spontaneous canine and pediatric high-grade glioma using imaging-based an arrayed CRISPR-Cas9 phenotypic screen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3106.